Deoxyribonuclease ii beta proteins and cdnas

ABSTRACT

The present invention provides cDNAs encoding deoxyribonuclease IIβ and isolated, purified deoxyribonuclease IIβ proteins. Antibodies against this protein and antisense agents targeted to a cDNA or corresponding mRNA encoding deoxyribonuclease IIβ are provided. In addition, methods of identifying and using modulators of deoxyribonuclease IIβ activity are described.

INTRODUCTION

[0001] This invention was made in the course of research sponsored by the National Institutes of Health. The U.S. Government may have certain rights in this invention.

BACKGROUND OF THE INVENTION

[0002] Controlled cell death is critical for the life of a human; too much cell death can cause the symptoms of cystic fibrosis and also lead to diseases such a neurodegeneration and acquired immune deficiency syndrome (AIDS). In contrast, too little cell death can lead to cancer or autoimmune diseases. Recent studies have defined the pathway of cell death as “apoptosis” and have identified some of the biochemical steps involved.

[0003] Apoptosis is a homeostatic mechanism involved in the controlled death of obsolete cells during metamorphosis, differentiation, cell turnover, and hormone mediated deletion of thymocytes (Wyllie et al. Int. Rev. Cytol. 1980 68:251-306). Apoptosis has also been identified as the mechanism of cell killing during growth factor withdrawal (Rodriguez-Tarduchy et al. EMBO J. 1990 9:2997-3002; McConkey et al. J. Biol. Chem. 1990 265:3009-3011), T-cell deletion, treatment with many cytotoxic agents (Cohen, J. J. and Duke, R. C. J. Immunol. 1984 132:38-42; Barry et al. Biochem. Pharmacol. 1990 40:2353-2362; Kaufmann, S. H. Cancer Res. 1989 49:5870-5878; and McConkey et al. Science 1988 242:256-259), and following hyperthermia (Barry et al. Biochem. Pharmacol. 1990 40:2353-2362; Lennon et al. Biochem. Soc. Trans. 1990 18:343-345; Takano et al. J. Pathol. 1991 163:329-336). observed during lens nuclear degeneration, and further support a role for this enzyme in mechanisms of cell death.

[0004] However, more recent results have implicated yet another endonuclease, referred to CAD or caspase-activated deoxyribonuclease, in apoptosis (Enari, M. et al. 1998 Nature 391:43-50). Thus, it remains to be determined which specific endonuclease is involved in apoptosis,

[0005] The enzyme referred to herein as deoxyribonuclease IIα (DNA IIα) was isolated and purified and the amino acid sequence determined (PCT/US97/18262). The DNA sequences for both the human and bovine proteins of DNase IIα have also been cloned (PCT/US97/18262). Use of DNA IIα in alleviating the suffering in patients with cystic fibrosis is also disclosed in this PCT application.

[0006] In cystic fibrosis, the lungs of patients fill with the remnants of dead cells, and in particular with the DNA from these dead cells. The presence of DNA makes the mucous plugs too viscous to expel. A suggested therapy for these symptoms is the use of DNase I to digest the DNA, thereby permitting expulsion of the mucous plugs. However, this therapy has not been particularly effective due to inactivity of the DNase I enzyme in the presence of actin, also present in the sputum.

[0007] It is believed that DNase II enzymes and variations thereof may provide a more effective therapeutic alternative.

[0008] Another isoform of the DNase II enzyme, referred to herein as deoxyribonuclease IIβ (DNase IIβ) has now been identified and the gene and protein sequences for the mouse and human homolog have been determined.

SUMMARY OF THE INVENTION

[0009] An object of the present invention is to provide a cDNA encoding deoxyribonuclease IIβ.

[0010] Another object of the present invention is to provide an isolated, purified deoxyribonuclease IIβ enzyme.

[0011] An isoform of this enzyme, referred to herein as deoxyribonuclease IIβ (DNase IIβ) has now been identified.

[0012] This full length gene for this isoform was first identified in mice by sequence comparison to expressed sequence tags entered in Genbank database which were similar, but not identical to DNase IIα. Oligonucleotide primers were synthesized to obtain the complete DNase IIβ mouse gene. The mouse DNase IIβ cDNA sequence is depicted as SEQ ID NO:1. The protein sequence of mouse DNase IIβ is depicted- in SEQ ID NO:2.

[0013] Information from the mouse sequence was used to isolate a human homolog of this gene. The human DNase IIβ cDNA sequence is depicted as SEQ ID NO:3. The protein sequence of human DNase IIβ encoded by the cDNA of SEQ ID NO:3 is depicted in SEQ ID NO:4.

[0014] Mouse and rat cDNAs of this homolog of DNase IIα have also been disclosed recently by Shiokawa and Tanuma (Nucleic Acid Res. 1999 27(20):4083-4089 and Biochemical and Biophysical Research Communications 1999 285:395-399).

[0015] It has been found that the DNase IIβ protein, like the DNase IIα protein, retains a critical histidine in the predicted active site thus indicating that these proteins have similar activities. However, there is sufficient difference in the region surrounding this histidine to suggest that their activities, and in particular their potential as a therapeutic for cystic fibrosis, may be slightly different. Specifically, the predicted active site of human DNase IIα is FNSTEDHSKWCV (SEQ ID NO:5) while the equivalent sequence in the human DNase IIβ isoform is FSSYQDHAKWCI (SEQ ID NO:6).

[0016] Further, it has now been found that DNase IIβ is expressed at high levels in human salivary glands and is secreted into the saliva.

[0017] Using fluorescence in situ hybridization (FISH), it has now been determined that the human DNase IIβ is located at DNase IIβ thereby protect cells from premature death. These antisense agents may therefore be useful in treating diseases resulting from too much cell death such as neurodegeneration and AIDS.

[0018] Accordingly, cDNAs of the present invention are useful in identifying agents which modulate, i.e., increase or decrease, apoptosis in cells. In this method, cells from a single culture are divided in two groups. The first group, referred to as the treated cells, are placed in contact with a test agent in a vehicle. The second group, referred to as untreated cells, are placed in contact with vehicle only. Treated and untreated cells are then transfected with the cDNA of the present invention and apoptosis in the treated and untreated cells is monitored to determine whether treating cells with the test agent modulates apoptosis in the cells.

[0019] In addition, the DNase IIβ proteins of the present invention or fragments thereof are useful as antigens to produce antibodies thereto. By “antibody” it is meant to include, but is not limited to, both polyclonal and monoclonal antibodies as well as chimeric, single chain, and humanized antibodies along with Fab fragments, or the product of a Fab expression library. Various techniques for producing such antibodies are well known in the art.

[0020] Polyclonal antibodies generated against DNase IIβ can be obtained by direct injection of the isolated, purified proteins of the present invention or fragments thereof into an animal, preferably a nonhuman. Such antibodies can then be used to isolate the enzyme from tissues expressing that enzyme.

[0021] For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Such techniques are used routinely by those skilled in the art. Some examples include, but are not limited to, the hybridoma technique, the trioma technique, the

[0022] The following nonlimiting examples are provided to further illustrate the present invention.

EXAMPLES Example1

[0023] Identification of Expressed Sequence Tags

[0024] The cDNA sequence of DNase IIα was submitted to the Genbank database on a regular basis for analysis against the rapidly accumlating data deposited therein to identify other cDNA and protein sequences with similarity to DNase IIα. An expressed sequence tag (EST) from mouse cDNA was indentified that has high similarity to DNase IIα. These EST sequences are random pieces of cDNA that have been partially sequence but have no known function. The identified mouse EST was purchased and completely sequenced. This sequencing revealed a complete cDNA sequence with considerable homology to DNase IIα, but with sufficient differences that it obviously represented a different gene.

[0025] Additional EST sequences from human tissues were found that had similarity to this mouse EST. However, upon sequencing they contained incomplete sequences. Specifically, EST # AI420898, whose sequence was deposited into Genbank on Mar. 28, 1999 was found to contain 932 bp of the gene referred to herein now as DNase IIβ. This sequence was cloned into pT7T3D-Pac vector from Pharmacia.

Example 2

[0026] Nucleic Acid Sequencing

[0027] Plasmid DNA obtained in Example 1 was sequenced using the Big-DyeDeoxy Terminator Cycle Sequencing Kit from Applied Biosystems, followed by analysis on an Applied Biosystems 370 DNA automated sequencer.

Example 3

[0028] Genomic Localization

[0029] Human genomic DNA was used as a substrate for PCR using oligonucleotide primers predicted from the homology with DNase

1 6 1 1224 DNA Mus sp. 1 tcccagtccc ctgcatggaa tgaaggccac agatagaaaa tgacagcaaa gcctctaaga 60 acagttcttt ctttgctctt ctttgccctc tctggggtcc tggggacacc agaaatctca 120 tgcagaaatg aatatggtga agctgtggac tggtttatct tttataagtt acccaaaagg 180 actagcaagg caagtgaaga ggcggggctg cagtacctgt acctggactc cacaagacaa 240 acctggaaca agagcctcta cctgattaac agcaccagga gtgctctggg gaggacctta 300 cagcatctgt atgacacaca taattccacg aatgacacag cctatctaat atacaacgat 360 ggtgtccctg gatctgtgaa ttacagcaga cagtatggac atgccaaagg tctgctggta 420 tggaacagaa cgcaggggtt ctggctgata cactctgttc ccaagtttcc cccagttcat 480 ggctatgagt acccaacctc ggggaggcga tatggacaaa ccggcatctg catcactttc 540 ggatacagcc agtttgagga aatagatttt cagctcttgg tcttacaacc aaacatctac 600 agctgcttca ttccaagcac ctttcactgg aaacttatct acatgccccg gatgtgtgcc 660 aactccagtt ccttaaagat ccctgtccgg tacctcgctg aactgcactc agcccagggt 720 ctaaacttcg tccattttgc aaaatcaagt ttttatactg atgacatctt tacaggatgg 780 atagctcaaa agttgaagac acatttgtta gcacaaacct ggcagaaaaa gaaacaagag 840 cttccttcaa actgttccct gccttaccat gtctacaaca tcaagtccat tggggtaact 900 tccaagtctt acttcagttc tcgccaagac cattccaaat ggtgtgtttc cataaagggc 960 tccgcaaatc gctggacctg cattggagac ctaaatcgaa gcctacacca agccttaaga 1020 ggtggaggat tcatctgtac aaagaatcac tacatttacc aggcatttca taaattatat 1080 ctccgttatg ggttctgtaa gtaaactcgg tgaaaggcca caccctctgt ccttgaaaac 1140 actggcactg gaacatctcg ccttggatct gttctccata atatcaaggc ttctgagtga 1200 gcacaacgta gcgtccaata aaag 1224 2 354 PRT Mus sp. 2 Met Thr Ala Lys Pro Leu Arg Thr Val Leu Ser Leu Leu Phe Phe Ala 1 5 10 15 Leu Ser Gly Val Leu Gly Thr Pro Glu Ile Ser Cys Arg Asn Glu Tyr 20 25 30 Gly Glu Ala Val Asp Trp Phe Ile Phe Tyr Lys Leu Pro Lys Arg Thr 35 40 45 Ser Lys Ala Ser Glu Glu Ala Gly Leu Gln Tyr Leu Tyr Leu Asp Ser 50 55 60 Thr Arg Gln Thr Trp Asn Lys Ser Leu Tyr Leu Ile Asn Ser Thr Arg 65 70 75 80 Ser Ala Leu Gly Arg Thr Leu Gln His Leu Tyr Asp Thr His Asn Ser 85 90 95 Thr Asn Asp Thr Ala Tyr Leu Ile Tyr Asn Asp Gly Val Pro Gly Ser 100 105 110 Val Asn Tyr Ser Arg Gln Tyr Gly His Ala Lys Gly Leu Leu Val Trp 115 120 125 Asn Arg Thr Gln Gly Phe Trp Leu Ile His Ser Val Pro Lys Phe Pro 130 135 140 Pro Val His Gly Tyr Glu Tyr Pro Thr Ser Gly Arg Arg Tyr Gly Gln 145 150 155 160 Thr Gly Ile Cys Ile Thr Phe Gly Tyr Ser Gln Phe Glu Glu Ile Asp 165 170 175 Phe Gln Leu Leu Val Leu Gln Pro Asn Ile Tyr Ser Cys Phe Ile Pro 180 185 190 Ser Thr Phe His Trp Lys Leu Ile Tyr Met Pro Arg Met Cys Ala Asn 195 200 205 Ser Ser Ser Leu Lys Ile Pro Val Arg Tyr Leu Ala Glu Leu His Ser 210 215 220 Ala Gln Gly Leu Asn Phe Val His Phe Ala Lys Ser Ser Phe Tyr Thr 225 230 235 240 Asp Asp Ile Phe Thr Gly Trp Ile Ala Gln Lys Leu Lys Thr His Leu 245 250 255 Leu Ala Gln Thr Trp Gln Lys Lys Lys Gln Glu Leu Pro Ser Asn Cys 260 265 270 Ser Leu Pro Tyr His Val Tyr Asn Ile Lys Ser Ile Gly Val Thr Ser 275 280 285 Lys Ser Tyr Phe Ser Ser Arg Gln Asp His Ser Lys Trp Cys Val Ser 290 295 300 Ile Lys Gly Ser Ala Asn Arg Trp Thr Cys Ile Gly Asp Leu Asn Arg 305 310 315 320 Ser Leu His Gln Ala Leu Arg Gly Gly Gly Phe Ile Cys Thr Lys Asn 325 330 335 His Tyr Ile Tyr Gln Ala Phe His Lys Leu Tyr Leu Arg Tyr Gly Phe 340 345 350 Cys Lys 3 1268 DNA Homo sapiens 3 atggggaaag tgtcctgctg tggcatgaaa taaatgaaac agaaaatgat ggcaagactg 60 ctaagaacat cctttgcttt gctcttcctt ggcctctttg gggtgctggg ggcagcaaca 120 atttcatgca gaaatgaaga agggaaagct gtggactggt ttacttttta taagttacct 180 aaaagacaaa acaaggaaag tggagagact gggttagagt acctgtacct agactctaca 240 actagaagct ggaggaagag tgagcaacta atgaatgaca ccaagagtgt tttgggaagg 300 acattacaac agctatatga agcatatgcc tctaagagta acaacacagc ctatctaata 360 tacaatgatg gagtccctaa acctgtgaat tacagtagaa agtatggaca caccaaaggt 420 ttactgctgt ggaacagagt tcaagggttc tggctgattc attccatccc tcagtttcct 480 ccaattccgg aagaaggcta tgattatcca cccacaggga gacgaaatgg acaaagtggc 540 atctgcataa ctttcaagta caaccagtat gaggcaatag attctcagct cttggtctgc 600 aaccccaacg tctatagctg ctccatccca gccacctttc accaggagct cattcacatg 660 ccccagctgt gcaccagggc cagctcatca gagattcctg gcaggctcct caccacactt 720 cagtcggccc agggacaaaa attcctccat tttgcaaagt cggattcttt tcttgacgac 780 atctttgcag cctggatggc tcaacggctg aagacacact tgttaacaga aacctggcag 840 cgaaaaagac aagagcttcc ttcaaactgc tcccttcctt accatgtcta caatataaaa 900 gcaattaaat tatcacgaca ctcttatttc agttcttatc aagatcacgc caagtggtgt 960 atttcccaaa agggcaccaa aaatcgctgg acatgtattg gagacctaaa tcggagtcca 1020 caccaagcct tcagaagtgg aggattcatt tgtacccaga attggcaaat ttaccaagca 1080 tttcaaggat tagtattata ctatgaaagc tgtaagtaaa cttggtgaaa ggacacaggt 1140 actatcattg aaaaccttga caatgggtct tcttccatta caccttcttt atattttaaa 1200 ggcctgtgaa tatacttata acctgcatat cacaaaataa aacatatttc tctcatgttt 1260 accattta 1268 4 357 PRT Homo sapiens 4 Met Met Ala Arg Leu Leu Arg Thr Ser Phe Ala Leu Leu Phe Leu Gly 1 5 10 15 Leu Phe Gly Val Leu Gly Ala Ala Thr Ile Ser Cys Arg Asn Glu Glu 20 25 30 Gly Lys Ala Val Asp Trp Phe Thr Phe Tyr Lys Leu Pro Lys Arg Gln 35 40 45 Asn Lys Glu Ser Gly Glu Thr Gly Leu Glu Tyr Leu Tyr Leu Asp Ser 50 55 60 Thr Thr Arg Ser Trp Arg Lys Ser Glu Gln Leu Met Asn Asp Thr Lys 65 70 75 80 Ser Val Leu Gly Arg Thr Leu Gln Gln Leu Tyr Glu Ala Tyr Ala Ser 85 90 95 Lys Ser Asn Asn Thr Ala Tyr Leu Ile Tyr Asn Asp Gly Val Pro Lys 100 105 110 Pro Val Asn Tyr Ser Arg Lys Tyr Gly His Thr Lys Gly Leu Leu Leu 115 120 125 Trp Asn Arg Val Gln Gly Phe Trp Leu Ile His Ser Ile Pro Gln Phe 130 135 140 Pro Pro Ile Pro Glu Glu Gly Tyr Asp Tyr Pro Pro Thr Gly Arg Arg 145 150 155 160 Asn Gly Gln Ser Gly Ile Cys Ile Thr Phe Lys Tyr Asn Gln Tyr Glu 165 170 175 Ala Ile Asp Ser Gln Leu Leu Val Cys Asn Pro Asn Val Tyr Ser Cys 180 185 190 Ser Ile Pro Ala Thr Phe His Gln Glu Leu Ile His Met Pro Gln Leu 195 200 205 Cys Thr Arg Ala Ser Ser Ser Glu Ile Pro Gly Arg Leu Leu Thr Thr 210 215 220 Leu Gln Ser Ala Gln Gly Gln Lys Phe Leu His Phe Ala Lys Ser Asp 225 230 235 240 Ser Phe Leu Asp Asp Ile Phe Ala Ala Trp Met Ala Gln Arg Leu Lys 245 250 255 Thr His Leu Leu Thr Glu Thr Trp Gln Arg Lys Arg Gln Glu Leu Pro 260 265 270 Ser Asn Cys Ser Leu Pro Tyr His Val Tyr Asn Ile Lys Ala Ile Lys 275 280 285 Leu Ser Arg His Ser Tyr Phe Ser Ser Tyr Gln Asp His Ala Lys Trp 290 295 300 Cys Ile Ser Gln Lys Gly Thr Lys Asn Arg Trp Thr Cys Ile Gly Asp 305 310 315 320 Leu Asn Arg Ser Pro His Gln Ala Phe Arg Ser Gly Gly Phe Ile Cys 325 330 335 Thr Gln Asn Trp Gln Ile Tyr Gln Ala Phe Gln Gly Leu Val Leu Tyr 340 345 350 Tyr Glu Ser Cys Lys 355 5 12 PRT Homo sapiens 5 Phe Asn Ser Thr Glu Asp His Ser Lys Trp Cys Val 1 5 10 6 12 PRT Homo sapiens 6 Phe Ser Ser Tyr Gln Asp His Ala Lys Trp Cys Ile 1 5 10 

What is claimed is:
 1. A cDNA encoding a deoxyribonuclease IIβ enzyme.
 2. The cDNA encoding the deoxyribonuclease IIβ enzyme of claim 1 comprising SEQ ID NO: 1 or
 3. 3. A vector comprising a cDNA of claim
 1. 4. An isolated and purified deoxyribonuclease IIβ enzyme.
 5. The isolated and purified deoxyribonuclease IIβ enzyme of claim 4 comprising SEQ ID NO: 2 or
 4. 6. An antibody against the deoxyribonuclease IIβ enzyme of claim
 4. 7. A method of determining DNase IIβ levels in selected cells comprising contacting selected cells with the antibody of claim 6 and detecting binding of said antibody to deoxyribonuclease IIβ enzyme in said selected cells.
 8. An antisense oligonucleotide targeted to a DNA or mRNA encoding the deoxyribonuclease IIβ enzyme of claim
 4. 9. A method of inhibiting expression of a deoxyribonuclease IIβ enzyme in cells comprising administering to cells an effective amount of the antisense oligonucleotide of claim 8 so that levels of deoxyribonuclease IIβ enzyme in cells are reduced.
 10. A method of digesting DNA comprising contacting DNA with an enzyme of claim
 4. 